Ontology highlight
ABSTRACT:
PROVIDER: PRJNA911478 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR22751355.fastq.gz | Fastqsanger.gz | |||
| SRR22751356.fastq.gz | Fastqsanger.gz | |||
| SRR22751357.fastq.gz | Fastqsanger.gz | |||
| SRR22751358.fastq.gz | Fastqsanger.gz | |||
| SRR22751359.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 17 |
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Project description:The cytochrome b6f (Cyt b6f) complex is a multisubunit protein complex in chloroplast thylakoid membranes required for photosynthetic electron transport. Here we report the isolation and characterization of the new tiny albino (nta1) mutant in Arabidopsis, which had severe defects in Cyt b6f accumulation and chloroplast development. Gene cloning unveiled that the nta1 phenotypes were caused by the disruption of a single nuclear gene, NTA1, which encodes an integral thylakoid membrane protein conserved across green algae and plants. Overexpression of NTA1 completely rescued the nta1 phenotypes, while knockout of NTA1 in wild type plants recapitulated the mutant phenotypes. Loss of NTA1 function severely impaired the accumulation of multiprotein complexes related to photosynthesis in thylakoid membranes, particularly the components of Cyt b6f. Furthermore, NTA1 was shown to directly interact with four subunits (Cyt b6/PetB, PetD, PetG and PetN) of Cyt b6f through the DUF1279 domain and C-terminal sequence to mediate their assembly. Taken together, our study identified NTA1 as a new and key regulator of chloroplast development, which plays essential roles in the assembly of Cyt b6f complex through interacting with multiple Cyt b6f subunits.
2023-02-22 | PXD038714 | Pride
Project description:It has been recently shown that SNRNP70, a major component of the spliceosome, as well as other splicing regulators are found in axons. To investigate the role of SNRNP70 in axons, we generated a zebrafish null mutant and found motor connectivity defects that can be partially rescued upon transgenic overexpression of cytoplasmic-only human SNRNP70 (cyt-hSNRNP70). To understand the molecular function of the cytoplasmic pool of this splicing protein, we performed this RNA-seq experiment with the aim to identify mRNA transcripts whose expression is regulated by the cytoplasmic pool of SNRNP70. To do that, we crossed heterozygous mutant animals that are also positive for the cyt-SNRNP70 transgene. We then split embryos into four groups: (i) sibling, (ii) siblings/cyt-hSNRNP70, (iii) null, (iv) null/cyt-hSNRNP70. Total RNA was extracted from each one of the four groups (three biological replicates per sample) and sequenced.
2022-10-31 | E-MTAB-12301 | biostudies-arrayexpress
Project description:Calcium acts as a universal second messenger to regulate gene expression in both developmental processes and responses to environmental stresses. Previous studies showed that a number of stimuli can induce calcium increases in the cytoplasm and nucleus, independently. However, the gene expression network deciphering [Ca2+]cyt and/or [Ca2+]nuc signaling pathway remain obscure. Using transgenic Arabidopsis containing a fusion protein, comprising rat parvalbumin (PV) with either a nuclear export sequence (PV-NES) or a nuclear localization sequence (NLS-PV), to selectively buffer the cytosolic or nucleosolic calcium, we identified the [Ca2+]cyt- or /and [Ca2+]nuc-regulated ABA- and MeJA-responsible genes with the Arabidopsis Genome Oligo array.
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Project description:For the detection of tiRNAs accumulated in Cyt c-IP vs tiRNAs in total cell lysates during hyperosmotic stress in the presence of angiogenin Total cell lysates from mouse embryonic fibroblasts treated with angiogenin under hyperosmotic stress. Lysates split into two parts: one part serveed as the total RNA, the other part served as Cyt c-IP fraction. Small RNAs were enriched from both parts and went through deep sequencing followed by bioinformatic analysis.
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Project description:Biogeographic 16S rRNA gene survey of the Grand River
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Project description:Today, many contaminants of emerging concern can be measured in waters across the United States, including the tributaries of the Great Lakes. However, just because the chemicals can be measured does not mean that they necessarily result in harm to fish and other aquatic species. Complicating risk assessment in these waters is the fact that aquatic species are encountering the chemicals as mixtures, which may have additive or synergistic risks that cannot be calculated using single chemical hazard and concentration-response information. We developed an in vitro effects-based screening approach to help us predict potential liver toxicity and cancer in aquatic organisms using water from specific Great Lakes tributaries: St. Louis River (MN), Bad River (WI), Fox River (WI), Manitowoc River (WI), Milwaukee River (WI), Indiana Harbor Canal (IN), St. Joseph River (MI), Grand River (MI), Clinton River (MI), River Rouge (MI), Maumee River (OH), Vermilion River (OH), Cuyahoga River (OH), Genesee River (NY), and Oswego River (NY). We exposed HepG2 cells for 48hrs to medium spiked with either field collected water (final concentration of environmental samples in the exposure medium were 75% of the field-collected water samples) or purified water. Using a deep neural network we clustered our collection sites from each tributary based on water chemistry. We also performed high throughput transcriptomics on the RNA obtained from the HepG2 cells. We used the transcriptomics data with our Bayesian Inferene for Sustance and Chemical Toxicity (BISCT) Bayesian Network for Steatosis to predict the probability of the field samples yielding a gene expression pattern consistent with predicting steatosis as an outcome. Surprisingly, we found that the probability of steatosis did not correspond to the surface water chemistry clustering. Our analysis suggests that chemical signatures are not informative in predicting biological effects. Furthermore, recent reports published after we obtained our samples, suggest that chemical levels in the sediment may be more relevant for predicting potential biological effects in the fish species developing tumors in the Great Lakes basin.
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Project description:Our aim is to identify circadian transcripts that are co-regulated with [Ca2+]cyt, with the eventual goal of identifying genetic regulators and targets for circadian oscillations of [Ca2+]cyt. We have identified two conditions in which [Ca2+]cyt behaves differently to other circadian outputs. 1. Treatment of plants with nicotinamide, a metabolic inhibitor of ADPR cyclase, abolishes the circadian oscillations of [Ca 2+]cyt. However, leaf movement, CCA1, LHY, TOC1 and CAB transcript abundance and CAB promoter activity are all rhythmic albeit with a longer period (Dodd et al., 2007). 2. The toc1-1 mutant, which shortens the circadian period of all other rhythms tested, has no effect on the period of [Ca2+]cyt oscillations (Xu et al., 2007). We will measure the circadian regulation of transcript abundance in wild type (C24), toc1-1 and nicotinamide (C24)-treated plants. Method: Wild type (C24) and toc1-1 seeds were sown on 1/2MS 0.8% agar plates and imbibed at 4 C for 48 hours. Seedlings were grown in LD cycles of 12hL:12hD at 19 C for 11 days to entrain the oscillator. Following transfer to LL at dawn on the 12th day, 50% of the wild type seedlings were dosed with 50 mM nicotinamide every 2 hours over the entire course of the experiment. Wild type, toc1-1 and nicotinamide-treated seedlings (approx. 100 for each sample, excluding roots) were harvested at 4 hour intervals from 49 to 93 hours in LL (12 time points covering the entire third and fourth circadian cycles). Two independent replicates of the whole experiment will be hybridised. 72 samples were used in this experiment.
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